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在海胆中,一个古老的发育基因调控网络的最近重排。

Recent reconfiguration of an ancient developmental gene regulatory network in Heliocidaris sea urchins.

机构信息

Department of Biology, Duke University, Durham, NC, USA.

BGI-Qingdao, BGI-Shenzhen, Qingdao, China.

出版信息

Nat Ecol Evol. 2022 Dec;6(12):1907-1920. doi: 10.1038/s41559-022-01906-9. Epub 2022 Oct 20.

Abstract

Changes in developmental gene regulatory networks (dGRNs) underlie much of the diversity of life, but the evolutionary mechanisms that operate on regulatory interactions remain poorly understood. Closely related species with extreme phenotypic divergence provide a valuable window into the genetic and molecular basis for changes in dGRNs and their relationship to adaptive changes in organismal traits. Here we analyse genomes, epigenomes and transcriptomes during early development in two Heliocidaris sea urchin species that exhibit highly divergent life histories and in an outgroup species. Positive selection and chromatin accessibility modifications within putative regulatory elements are enriched on the branch leading to the derived life history, particularly near dGRN genes. Single-cell transcriptomes reveal a dramatic delay in cell fate specification in the derived state, which also has far fewer open chromatin regions, especially near conserved cell fate specification genes. Experimentally perturbing key transcription factors reveals profound evolutionary changes to early embryonic patterning events, disrupting regulatory interactions previously conserved for ~225 million years. These results demonstrate that natural selection can rapidly reshape developmental gene expression on a broad scale when selective regimes abruptly change. More broadly, even highly conserved dGRNs and patterning mechanisms in the early embryo remain evolvable under appropriate ecological circumstances.

摘要

发育基因调控网络 (dGRN) 的变化是生命多样性的基础,但调控相互作用的进化机制仍知之甚少。具有极端表型分歧的密切相关物种为 dGRN 的变化及其与生物体特征适应性变化的关系提供了一个宝贵的遗传和分子基础的窗口。在这里,我们分析了两个表现出高度分化生活史的海胆物种和一个外群物种在早期发育过程中的基因组、表观基因组和转录组。在导致衍生生活史的分支上,假定的调控元件内的正选择和染色质可及性修饰富集,特别是在 dGRN 基因附近。单细胞转录组揭示了在衍生状态下细胞命运特化的急剧延迟,而且开放染色质区域也少得多,特别是在保守的细胞命运特化基因附近。实验性地扰动关键转录因子揭示了早期胚胎模式形成事件的深刻进化变化,破坏了此前保守了约 2.25 亿年的调控相互作用。这些结果表明,当选择机制突然改变时,自然选择可以迅速在广泛范围内重塑发育基因表达。更广泛地说,即使是在早期胚胎中高度保守的 dGRN 和模式形成机制,在适当的生态环境下仍然是可进化的。

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